Name Mode Size
R 040000
inst 040000
man 040000
tests 040000
vignettes 040000
.Rbuildignore 100644 0 kb
.gitignore 100644 0 kb
.travis.yml 100644 0 kb
DESCRIPTION 100644 2 kb
NAMESPACE 100644 2 kb 100644 2 kb
# MAGAR [![Build Status](]( [![License: GPL v3](]( ![]( ## Short description *MAGAR* (Methylation-Aware Genotype Association in R) is an R package for computing DNA methylation quantitative trait loci (methQTL) from DNA methylation and matched genotyping data. The tool employs a two-stage approach to compute methQTL: - CpG correlation blocks are computed to mimic DNA methylation haplotypes. The correlation blocks are computed from CpGs that are highly correlated across the samples. - For each correlation block, a representative CpG (tag-CpG) is computed and used in a linear modeling strategy (or alternatively with [*fastQTL*]( to determine significant associations between genotype variation and changes in DNA methylation of particular CpGs. The package furthermore uses established software tools for handling DNA methylation and genotyping data, including [*RnBeads*](, [*PLINK*](, and [*CRLMM*]( Thus, raw DNA methylation data (IDAT, BED files) and genotyping data (IDAT, PLINK files) can be used as input. ## Installation The package needs some Bioconductor dependencies, most notably *RnBeads*, which can be directly installed from the [*RnBeads* website]( Atfer instaling *RnBeads*, *MAGAR* can be installed in a R session using the ```devtools``` package ```r source("") if(!requireNamespace("devtools")) install.packages("devtools") devtools::install_github("MPIIComputationalEpigenetics/MAGAR") ``` ## Documentation You can find a detailed information for *MAGAR* [here](vignettes/MAGAR.Rmd) ## Citation Scherer, M., Gasparoni, G., Rahmouni, S. et al. Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR. Epigenetics & Chromatin 14, 44 (2021). [doi:10.1186/s13072-021-00415-6]( ## Contact You can contact [Michael Scherer]( for reporting bugs, feature requests or questions.